Global methods for genomic analysis have provided useful insights into the pathophysiology of cancer and other diseases or conditions with a genetic component. Such methods include karyotyping, determination of ploidy, comparative genomic hybridizaton (CGH), representational difference analysis (RDA) (see, e.g., U.S. Pat. No. 5,436,142), and analysis of genomic representations (WO 99/23256, published May 14, 1999). Generally, these methods involve either using probes to interrogate the expression of particular genes or examining changes in the genome itself.
Using oligonucleotide arrays, these methods can be used to obtain a high resolution global image of genetic changes in cells. However, these methods require knowledge of the sequences of the particular probes. This is particularly limiting for cDNA arrays because such arrays only interrogate a limited set of genes. They also are limiting for genome-wide screening because many oligonucleotides designed for an array may be unrepresented in the interrogated population, resulting in inefficient or ineffective analysis.